Chief Judicial Magistrate Anupama Bijlani has admitted the application moved by Lalit Boda, the then forest officer who had registered the case against Khan for alleged poaching of black bucks in 1998.
The matter has been listed for hearing on April 29.
However, Khan's counsel H M Saraswat said they had mentioned in the exemption application that Khan had a problem in his ear and has been recommended not to travel by air.
Boda in his application cited a news report showing Khan shooting for his upcoming film, Bajrangi Bhaijan, in Jammu and Kashmir.
He alleged that by seeking exemption on health grounds, Khan has given wrong facts and has misled the court. Boda sought stringent action against Khan for misleading the court.
A case had been registered against Khan by the forest department under the Arms Act mentioning that licence of the arms used by Khan during alleged poaching of black bucks at village Kankani near Jodhpur on the intervening night of 1-2 October, 1998, had expired and hence the actor had been using the arms illegally.